Bioinformatics secondary analysis tools that process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy and 100% consistency.


Sentieon provides complete solutions for secondary DNA analysis. Its software improves upon BWA, GATK, Mutect, and Mutect2 based pipelines. The Sentieon tools are deployable on any generic-CPU-based computing system. Sentieon products are already installed at over 100 sites worldwide. Its products have been extensively tested and validated by numerous customers, and have run through tens of thousands of genome datasets, the majority of which are WGS or WES, with a total of over 2 peta-basepairs of DNA.
  • Sentieon DNAseq
    Sentieon DNAseq implements the same mathematics used in the Broad Institute’s BWA-GATK HaplotypeCaller 3.x Best Practice Workflow pipeline, but with more efficient computing algorithms and enterprise-strength software implementation. Compared to the BWA-GATK pipeline, the Sentieon DNAseq pipeline is 10X faster measured in terms of total core hours for processing from FASTQ to VCF, on the same generic-CPU-based system with no special hardware requirements. This includes a computing efficiency enhancement to BWA-MEM. For aligned-BAM-to-VCF processing, Sentieon DNAseq is 20X-50X faster than GATK. The software is also able to do joint call on over 100K samples together without intermediate file merging, saving time and effort.
    • Identical mathematics as Broad Institute’s BWA-GATK Best Practice Workflow, but over 10X faster FASTQ-to-VCF, 20X-50X faster BAM-to-VCF, measured in core-hours
    • No run-to-run difference, no down-sampling in high coverage regions
    • 100K samples joint-calling without intermediate file merging
    • Pure software solution running on any generic-CPU-based system
  • Sentieon TNseq
    Sentieon TNseq is a tumor-normal pair somatic variant detection product with modes that can match either MuTect (calls SNV in somatic variants) or MuTect2 (MuTect2 is currently in beta release by the Broad Institute; it calls both SNV and INDEL in somatic variants) in the same sense as Sentieon DNAseq matches BWA-GATK: identical mathematics, but more efficient computing algorithms and enterprise-strength software implementation.
    • Identical mathematics as Broad Institute’s Mutect and MuTect2, but over 10X faster FASTQ-to-VCF, measured in core-hours
    • No run-to-run difference, no down-sampling in high coverage regions
    • Pure software solution running on any generic-CPU-based system

Use Cases

Align & Variant Calling

Sentieon’s secondary analysis pipeline has proven to be powerful to call single nucleotide variations and INDELs for germline and cancer data...

It provides significant speed advantages over existing methods, without sacrificing precision and accuracy. Sentieon’s products are highly synergistic with Golden Helix Copy Number Caller VS-CNV. The two products combined provide the most complete secondary analysis solution in the industry. While this solution will benefit all of our users, we are particularly excited for our customers that operate in a high-throughput environment.

Case Studies

We know our software will exceed your expectations. But don't just take it from us, see what our customers have benefitted from it.

Recommended Learning Materials

We have a variety of supplemental learning materials that are an excellent resource for anyone interested in the industry or our software solutions. Here are some of our recommended materials for you to check out related to VarSeq!


Check out our free eBooks on a variety of different topics:

Other Resources

Learn more about Sentieon by checking out these informative whitepapers!

Try Sentieon for Free

Did you know we offer complimentary trials of our software? No restricted features, no sample data - you get to try all the features of Sentieon with your data and see how it works!

If you are interested in a trial, please fill out the form below, and we will send you the details!

Technical Specifications

4 GB of RAM

Multicore CPU

100GB of space available for annotations and projects


If you are working with whole exomes or genomes, especially if or hundreds to thousands of samples, we suggest a high-memory configuration and plenty of storage capacity:

16GB+ of RAM (32GB for Servers)

8+ CPU Cores

1TB of space available for annotations and projects


The following operating systems are supported:

64-bit Windows 10 or later

Linux Ubuntu 18.04 (64-bit only)

RedHat/CentOS 7.x, Debian 7.7, OpenSUSE-13.2


The software only needs to make outgoing connections on standard HTTP/HTTPS ports and protocols. If a local firewall is installed that prevents these types of outgoing connections (this is very uncommon), firewall rules will need to be created to whitelist the software.

Note we have run into numerous issues where aggressive anti-virus programs prevent the product from performing normal operations such as opening files and logging in. You may need to whitelist Golden Helix executables or disable these tools to perform your analytics.